5-25760570-G-T

Variant names:

• chr5-25760570-G-T
• rs7727656

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.632 in 152,062 control chromosomes in the GnomAD database, including 32,703 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (32703 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96096 AN: 151944 Hom.: 32691 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.644

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.632 AC: 96130 AN: 152062 Hom.: 32703 Cov.: 33 AF XY: 0.628 AC XY: 46691 AN XY: 74332

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.647

Alfa AF: 0.745 Hom.: 97114

Bravo AF: 0.620

Asia WGS AF: 0.577 AC: 2005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7727656; hg19: chr5-25760679;